scholarly journals Solvation free energies for periodic surfaces: comparison of implicit and explicit solvation models

2016 ◽  
Vol 18 (46) ◽  
pp. 31850-31861 ◽  
Author(s):  
Stephan N. Steinmann ◽  
Philippe Sautet ◽  
Carine Michel
Keyword(s):  
Free Energy ◽  
Liquid Interfaces ◽  
Free Energies ◽  
Periodic Surfaces ◽  
Solvation Energies ◽  
Solvation Models ◽  
Implicit And Explicit ◽  
Solvation Free Energies ◽  
Solid Liquid ◽  
Explicit Solvation

A strategy based on molecular mechanics free energy of perturbation, seeded by quantum mechanics, is presented to take solvation energies into account in the context of periodic, solid–liquid interfaces.

Quantitative Evaluation of the Interfacial Free Energies at A Solid-Liquid Lamellar Eutectic Interface

1981 ◽  
Vol 12 ◽  
Author(s):  
W. F. Kaukler ◽  
J. W. Rutter
Keyword(s):  
Free Energy ◽  
Solid Phase ◽  
Interfacial Free Energy ◽  
Eutectic System ◽  
Liquid Interfaces ◽  
Free Energies ◽  
Two Phases ◽  
Interfacial Free Energies ◽  
The Individual ◽  
Solid Liquid

The solid-liquid interfacial free energies of each of the individual phases comprising the eutectic system, Carbon Tetrabromide-Hexachloroethane, were measured as a function of composition using a “grain boundary groove” technique. Thermodynamic data were combined with groove shape measurements made from high resolution optical photomicrographs of the solid-liquid interfaces to give the interfacial free energy data. An interfacial free energy balance at the eutectic trijunction was performed to obtain all the forces acting on that point. The three interphase interfacial free energies at the eutectic trijunctions as well as a solid-solid phase boundary torque were evaluated.It was found that the solid-liquid interfacial free energies of the two phases of the eutectic could be evaluated from photomicrographs of growing or stationary eutectic interfaces. In addition, it was found that for a substantial range of freezing conditions the eutectic interface shape can be predicted from a knowledge of the interfacial free energies alone.

scholarly journals Thermodynamic Decomposition of Solvation Free Energies with Particle Mesh Ewald and Long-Range Lennard-Jones Interactions in Grid Inhomogeneous Solvation Theory

2020 ◽  
Author(s):  
Lieyang Chen ◽  
Anthony Cruz ◽  
Daniel R. Roe ◽  
Andrew Simmonett ◽  
Lauren Wickstrom ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Long Range ◽  
Free Energies ◽  
Particle Mesh Ewald ◽  
Lennard Jones ◽  
Current Implementation ◽  
Solvation Energies ◽  
Solvation Free Energies ◽  
Solvation Theory

Grid Inhomogeneous Solvation Theory (GIST) maps out solvation thermodynamic properties on a fine meshed grid and provides a statistical mechanical formalism for thermodynamic end-state calculations. However, differences in how long-range non-bonded interactions are calculated in molecular dynamics engines and in the current implementation of GIST have prevented precise comparisons between free energies estimated using GIST and those from other free energy methods such as thermodynamic integration (TI). Here, we address this by presenting PME-GIST, a formalism by which particle mesh Ewald (PME) based electrostatic energies and long-range Lennard-Jones (LJ) energies are decomposed and assigned to individual atoms and the corresponding voxels they occupy in a manner consistent with the GIST approach. PME-GIST yields potential energy calculations that are precisely consistent with modern simulation engines and performs these calculations at a dramatically faster speed than prior implementations. Here, we apply PME-GIST end-states analyses to 32 small molecules whose solvation free energies are close to evenly distributed from 2 kcal/mol to -17 kcal/mol and obtain solvation energies consistent with TI calculations (R2 = 0.99, mean unsigned difference 0.8 kcal/mol). We also estimate the entropy contribution from the 2nd and higher order entropy terms that are truncated in GIST by the differences between entropies calculated in TI and GIST. With a simple correction for the high order entropy terms, PME-GIST obtains solvation free energies that are highly consistent with TI calculations (R2 = 0.99, mean unsigned difference = 0.4 kcal/mol) and experimental results (R2 = 0.88, mean unsigned difference = 1.4 kcal/mol). The precision of PME-GIST also enables us to show that the solvation free energy of small hydrophobic and hydrophilic molecules can be largely understood based on perturbations of the solvent in a region extending a few solvation shells from the solute. We have integrated PME-GIST into the open-source molecular dynamics analysis software CPPTRAJ.

scholarly journals Thermodynamic Decomposition of Solvation Free Energies with Particle Mesh Ewald and Long-Range Lennard-Jones Interactions in Grid Inhomogeneous Solvation Theory

2020 ◽  
Author(s):  
Lieyang Chen ◽  
Anthony Cruz ◽  
Daniel R. Roe ◽  
Andrew Simmonett ◽  
Lauren Wickstrom ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Long Range ◽  
Free Energies ◽  
Particle Mesh Ewald ◽  
Lennard Jones ◽  
Current Implementation ◽  
Solvation Energies ◽  
Solvation Free Energies ◽  
Solvation Theory

Grid Inhomogeneous Solvation Theory (GIST) maps out solvation thermodynamic properties on a fine meshed grid and provides a statistical mechanical formalism for thermodynamic end-state calculations. However, differences in how long-range non-bonded interactions are calculated in molecular dynamics engines and in the current implementation of GIST have prevented precise comparisons between free energies estimated using GIST and those from other free energy methods such as thermodynamic integration (TI). Here, we address this by presenting PME-GIST, a formalism by which particle mesh Ewald (PME) based electrostatic energies and long-range Lennard-Jones (LJ) energies are decomposed and assigned to individual atoms and the corresponding voxels they occupy in a manner consistent with the GIST approach. PME-GIST yields potential energy calculations that are precisely consistent with modern simulation engines and performs these calculations at a dramatically faster speed than prior implementations. Here, we apply PME-GIST end-states analyses to 32 small molecules whose solvation free energies are close to evenly distributed from 2 kcal/mol to -17 kcal/mol and obtain solvation energies consistent with TI calculations (R2 = 0.99, mean unsigned difference 0.8 kcal/mol). We also estimate the entropy contribution from the 2nd and higher order entropy terms that are truncated in GIST by the differences between entropies calculated in TI and GIST. With a simple correction for the high order entropy terms, PME-GIST obtains solvation free energies that are highly consistent with TI calculations (R2 = 0.99, mean unsigned difference = 0.4 kcal/mol) and experimental results (R2 = 0.88, mean unsigned difference = 1.4 kcal/mol). The precision of PME-GIST also enables us to show that the solvation free energy of small hydrophobic and hydrophilic molecules can be largely understood based on perturbations of the solvent in a region extending a few solvation shells from the solute. We have integrated PME-GIST into the open-source molecular dynamics analysis software CPPTRAJ.

scholarly journals Improved prediction of solvation free energies by machine-learning polarizable continuum solvation model

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Amin Alibakhshi ◽  
Bernd Hartke
Keyword(s):  
Machine Learning ◽  
Free Energy ◽  
Solvation Free Energy ◽  
Continuum Solvation ◽  
Free Energies ◽  
Solvation Model ◽  
Continuum Solvation Model ◽  
Solvation Models ◽  
Solvation Free Energies ◽  
Polarizable Continuum

AbstractTheoretical estimation of solvation free energy by continuum solvation models, as a standard approach in computational chemistry, is extensively applied by a broad range of scientific disciplines. Nevertheless, the current widely accepted solvation models are either inaccurate in reproducing experimentally determined solvation free energies or require a number of macroscopic observables which are not always readily available. In the present study, we develop and introduce the Machine-Learning Polarizable Continuum solvation Model (ML-PCM) for a substantial improvement of the predictability of solvation free energy. The performance and reliability of the developed models are validated through a rigorous and demanding validation procedure. The ML-PCM models developed in the present study improve the accuracy of widely accepted continuum solvation models by almost one order of magnitude with almost no additional computational costs. A freely available software is developed and provided for a straightforward implementation of the new approach.

scholarly journals Thermodynamic Decomposition of Solvation Free Energies with Particle Mesh Ewald and Long-Range Lennard-Jones Interactions in Grid Inhomogeneous Solvation Theory

2020 ◽  
Author(s):  
Lieyang Chen ◽  
Anthony Cruz ◽  
Daniel R. Roe ◽  
Andrew Simmonett ◽  
Lauren Wickstrom ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Long Range ◽  
Free Energies ◽  
Particle Mesh Ewald ◽  
Lennard Jones ◽  
Current Implementation ◽  
Solvation Energies ◽  
Solvation Free Energies ◽  
Solvation Theory

Grid Inhomogeneous Solvation Theory (GIST) maps out solvation thermodynamic properties on a fine meshed grid and provides a statistical mechanical formalism for thermodynamic end-state calculations. However, differences in how long-range non-bonded interactions are calculated in molecular dynamics engines and in the current implementation of GIST have prevented precise comparisons between free energies estimated using GIST and those from other free energy methods such as thermodynamic integration (TI). Here, we address this by presenting PME-GIST, a formalism by which particle mesh Ewald (PME) based electrostatic energies and long-range Lennard-Jones (LJ) energies are decomposed and assigned to individual atoms and the corresponding voxels they occupy in a manner consistent with the GIST approach. PME-GIST yields potential energy calculations that are precisely consistent with modern simulation engines and performs these calculations at a dramatically faster speed than prior implementations. Here, we apply PME-GIST end-states analyses to 32 small molecules whose solvation free energies are close to evenly distributed from 2 kcal/mol to -17 kcal/mol and obtain solvation energies consistent with TI calculations (R2 = 0.99, mean unsigned difference 0.8 kcal/mol). We also estimate the entropy contribution from the 2nd and higher order entropy terms that are truncated in GIST by the differences between entropies calculated in TI and GIST. With a simple correction for the high order entropy terms, PME-GIST obtains solvation free energies that are highly consistent with TI calculations (R2 = 0.99, mean unsigned difference = 0.4 kcal/mol) and experimental results (R2 = 0.88, mean unsigned difference = 1.4 kcal/mol). The precision of PME-GIST also enables us to show that the solvation free energy of small hydrophobic and hydrophilic molecules can be largely understood based on perturbations of the solvent in a region extending a few solvation shells from the solute. We have integrated PME-GIST into the open-source molecular dynamics analysis software CPPTRAJ.

scholarly journals Hydration Thermodynamics of Non-Polar Aromatic Hydrocarbons: Comparison of Implicit and Explicit Solvation Models

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 2927 ◽  
Author(s):  
Hankyul Lee ◽  
Hyung-Kyu Lim ◽  
Hyungjun Kim
Keyword(s):  
Mean Field ◽  
Physical Nature ◽  
Free Energies ◽  
Implicit Model ◽  
Polar Solutes ◽  
Cause Of Error ◽  
Solvation Models ◽  
Poisson Boltzmann ◽  
Implicit And Explicit ◽  
Explicit Solvation

The precise description of solute-water interactions is essential to understand the chemo-physical nature in hydration processes. Such a hydration thermodynamics for various solutes has been explored by means of explicit or implicit solvation methods. Using the Poisson-Boltzmann solvation model, the implicit models are well designed to reasonably predict the hydration free energies of polar solutes. The implicit model, however, is known to have shortcomings in estimating those for non-polar aromatic compounds. To investigate a cause of error, we employed a novel systematic framework of quantum-mechanical/molecular-mechanical (QM/MM) coupling protocol in explicit solvation manner, termed DFT-CES, based on the grid-based mean-field treatment. With the aid of DFT-CES, we delved into multiple energy parts, thereby comparing DFT-CES and PB models component-by-component. By applying the modified PB model to estimate the hydration free energies of non-polar solutes, we find a possibility to improve the predictability of PB models. We expect that this study could shed light on providing an accurate route to study the hydration thermodynamics for various solute compounds.

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